I don't quite agree with you when you say that the past perfect is used in stories instead of the past simple. The past simple is the appropriate tense for telling stories. This said, we use the past perfect to refer to actions/events that happened before the actions/events we are talking about. If for instance you say:"When Hyena arrived, Hare ran into the bus", you mean that Hyena arrived before Hare ran into the bush. But you say"Hyena arrived but Hare had run into the bush", you mean that Hyena arrived after the action (Hare ran into the bush).
Does it make sense for you?